I had always thought (as others comment) that $1 and friends weren't reliable after a failed match, but I note that the following was added to perlre beginning with 5.8.1:

NOTE: failed matches in Perl do not reset the match variables, which makes easier to write code that tests for a series of more specific cases and remembers the best match.

But perlre also says:

The numbered match variables ($1, $2, $3, etc.) and the related punctuation set ($+, $&, $`, $', and $^N) are all dynamically scoped until the end of the enclosing block or until the next successful match, whichever comes first. (See perlsyn/"Compound Statements".)

and in your case you are actually leaving and reentering the enclosing block, which seems to make a difference:

$ perl -we'$_="FOO"; /^([A-Z]+)$/, print $1; $_="Foo"; /^([A-Z]+)$/; p
+rint $1'
FOOFOO
$ perl -we'for ("FOO","Foo") {/^([A-Z]+)$/; print $1 }'
FOOF
[download]

though it would be nice if it failed consistenly rather than sometimes working and other times not.